Genetic Susceptibility Of Cytotoxic T Lymphocyte-Associated Antigen 4 Gene Polymorphism In The Onset Of Arthritis

ABSTRACTCytotoxic T lymphocyte-associated antigen 4 (CTLA-4) gene plays a vital role in the activation of T-cells as a down regulator. CTLA-4 gene polymorphisms have implicated a potential risk factor for autoimmune disorders like arthritis. Therefore the current study was designed to determine the association of CTLA-4 gene polymorphism in the onset of rheumatoid and osteoarthritis in Pakistani individuals. Genotyping was performed on 300 RA, 316 OA, and 412 control subjects by direct sequencing method as well as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. It was observed that allelic and genotypic frequency of rs5742909, rs231775, rs4553808, rs733618, and rs3087243 were significantly varied among patients and controls and considered as a significant risk factor in the onset of RA as well as OA. However, no mutation was identified on the rs11571317 polymorphic site. Haplotype CAGTCA and CAG TCG act as a protectant against disease onset whereas CAACCG was significant in disease onset. Mutation on rs231775 polymorphic site lead to the change of threonine into alanine It was concluded that CTLA-4 gene polymorphism is a significant risk factor in the onset of RA as well as OA. Large scale survey is required for the screening of the genetic markers for pre-diagnosis of the disease.SUMMARY STATEMENTThe study summarized that CTLA-4 gene polymorphism plays a key role in the arthritis onset in Pakistani population.

Polymorphic site index curves for Beech (Fagus sylvatica L.) in Central and Eastern Serbia

This study was mainly aimed at constructing polymorphic site index curves for beech in the central (Rudnik mountain – RU, about 15,000 ha) and eastern (Žagubica – ŽA, about 7,000 ha) part of its distribution in Serbia. To obtain suitable height-age data and evaluate the best-fit growth model we used 107 felled dominant beech trees. The Korf, Korsun and Chapman-Richards growth functions per site class were first parameterized and then mutually compared with respect to residual statistics and the significance of their parameters. They were additionally parameterized in line with empirical data on the value and age of the culmination of current annual height increment (CAI_h). The obtained results indicated that the Chapman-Richards growth function showed the best results both by statistical (residuals standard error, significance of the parameters, distribution of residuals, and homoscedasticity) and by empirical criteria (the CAI_h culmination time, the maximal values of the CAI_h, and the attained height of trees at a certain age) of the height-age beech modelling in the analyzed regions. The obtained polymorphic site index curves which classify sites with regard to their productivity can be very helpful in planning appropriate silvicultural treatments, and for decision-making in forest management planning, forest policy and ecology and, consequently, in the sustainable management of beech forests in Serbia and some neighbouring countries with a similar forestry sector development.

Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization

Background The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. Results Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. Conclusions The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors.

The cytochrome 11B2 aldosterone synthase gene rs1799998 single nucleotide polymorphism determines elevated aldosterone, higher blood pressure, and reduced glomerular filtration, especially in diabetic female patients

Objective. The cytochrome 11B2 aldosterone synthase gene (CYP11B2) that links to aldosterone synthase enzyme synthesis changes and blood pressure regulation is of particular interest among the renin-angiotensin-aldosterone system encoding genes.Methods. One-hundred hypertensive patients with target-organ damaging (2nd stage), moderate, high or very high cardiovascular risk were involved in the case-control study. Mean age was 59.87±8.02 years. Diabetes Mellitus type 2 (DM2) was in 28 persons. Chronic kidney disease (CKD) was diagnosed in 29 persons according to the National Kidney Foundation recommendations (2012) after glomerular filtration rate (GFR) decline <60 ml/min/1.73m2 for ≥3 months (measured by CKD-EPI equations). Aldosterone, cystatin-C, and creatinine levels were measured in serum. Control group included 48 practically healthy persons of relevant age. Gene’s nucleotide polymorphism CYP11B2 (-344C/T) was examined by polymerase chain reaction.Results. CKD evolution in hypertensive patients followed by higher systolic and diastolic blood pressure (SBP, DBP) values increased creatinine, cystatin-C, and aldosterone serum concentrations by 28.76%, 28.41% and 29.43% (р<0.05), respectively. Polymorphic site of CYP11B2 (rs1799998) gene is associated with SBP and DBP increase (p<0.05), reduced GFR preferably calculated by CKDEPI-cystatin C (F=10.79–14.45; p<0.001) and elevated aldosterone content (F=55.84; p<0.001), creatinine and cystatin-С as well (F=4.16–5.08; p<0.05) mainly in the ТТ-genotype female carriers (p<0.001). Hypertensive women with DM2 demonstrated stronger relations of CYP11B2 gene polymorphic site with the increased aldosterone content (F=47.52; p<0.001), than women without DM2 (p<0.001) and male patients (p=0.014).Conclusions. Genetic variations involving CYP11B2 might influence the kidney function, hypertension course, and severity via aldosterone secretion upregulation.

Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies

ABSTRACTDespite the potential relevance to clinical outcome, intra-host dynamics of SARS-CoV-2 are unclear. Here, we quantify and characterize intra-host variation in SARS-CoV-2 raw sequence data uploaded to SRA as of 14 April 2020, and compare results between two sequencing methods (amplicon and RNA-Seq). Raw fastq files were quality filtered and trimmed using Trimmomatic, mapped to the WuhanHu1 reference genome using Bowtie2, and variants called with bcftools mpileup. To ensure sufficient coverage, we only included samples with 10X coverage for >90% of the genome (n=406 samples), and only variants with a depth >=10. Derived (i.e. non-reference) alleles were found at 408 sites. The number of polymorphic sites (i.e. sites with multiple alleles) within samples ranged from 0-13, with 72% of samples (295/406) having at least one polymorphic site. Correlation between number of polymorphic sites and coverage was very low for both sequencing methods (R2 < 0.1, p < 0.05). Polymorphisms were observed >1 sample at 66 sites (range: 2-38 samples). The minor allele frequency (MAF) at each shared polymorphic site was 0.03% - 48.5%. 33/66 sites occurred in ORF1a1b, and 37/66 changes were non-synonymous. At 10/66 sites, derived alleles were found in samples sequenced using both methods. Polymorphic amplicon samples were found at 10/10 positions, while polymorphic RNA-Seq samples were found at 7/10 positions. In conclusion, our results suggest that intra-host variation is prevalent among clinical samples. While mutations resulting from amplification and/or sequencing errors cannot be excluded, the observation of shared polymorphic sites with high MAF across multiple samples and sequencing methods is consistent with true underlying variation. Further investigation into intra-host evolutionary dynamics, particularly with longitudinal sampling, is critical for broader understanding of disease progression.

Role of XmnI polymorphism in HbF induction in HbE/β and β-thalassaemia patients

Background: Thalassaemia is one of the most common genetic blood disorders worldwide. Patients with β-thalassaemia major and HbE/β-thalassaemia are blood transfusion dependent. Foetal haemoglobin or HbF can play a role in disease manifestations in these patients and there is evidence that a homozygous state for XmnI polymorphic site, associated with increased expression of Gγ-gene, may play an important role among other factors in ameliorating the clinical severity of homozygous β-thalassaemia and thalassaemia intermedia. The aim of this review was to provide a comprehensive review of the role of XmnI polymorphic site for increased HbF production in HbE/β and β-thalassaemia patients. Methods: Published literatures were reviewed on the allelic frequency of Xmn1 polymorphism and its effect on HbF induction among thalassaemia patients of different countries. Results: In all β-thalassaemias, Hb F levels are relatively increased due to the selective survival of the erythroid precursors that synthesize relatively more γ-chains. The expression of HbF level is dominated by three different loci: HBG2: γ -158C>T, BCL11A, and HBS1L-MYB intergenic region. Genetic determinants influencing Hb F response can be within the β-globin complex or trans-acting. The published literature showed that the C>T substitution (rs7482144) at position –158 of the Gγ-globin gene, referred to as the XmnI-Gγ polymorphism, is a common sequence variant in all population groups, present at a frequency of 0.32 to 0.35. It was found in some studies, response to Hydroxyurea (HU) has been shown to be largely associated with the presence of the C>T polymorphism at -158 XmnI site (HBG2:c.- 53-158C>T) upstream of the Gγ-globin gene and HU therapy exerts a 2- to 9- fold increase in γ-mRNA expression in β-thalassaemia patients. Conclusion: A number of various study groups around the world suggests that XmnI polymorphism is an important key regulator of disease severity of HbE/β and β-thalassaemia patients.